1 #ifndef Mothur_sortseqscommand_h
2 #define Mothur_sortseqscommand_h
9 // Created by Sarah Westcott on 2/3/12.
10 // Copyright (c) 2012 Schloss Lab. All rights reserved.
15 #include "command.hpp"
17 class SortSeqsCommand : public Command {
21 SortSeqsCommand(string);
25 vector<string> setParameters();
26 string getCommandName() { return "sort.seqs"; }
27 string getCommandCategory() { return "Sequence Processing"; }
28 string getOutputFileNameTag(string, string);
29 string getHelpString();
30 string getCitation() { return "http://www.mothur.org/wiki/Sort.seqs"; }
31 string getDescription() { return "puts sequences from a fasta, name, group, quality, flow or taxonomy file in the same order"; }
34 void help() { m->mothurOut(getHelpString()); }
38 map<string, int> names;
39 string accnosfile, fastafile, namefile, groupfile, countfile, taxfile, qualfile, flowfile, outputDir;
41 vector<string> outputNames;